Repitools: Epigenomic tools

Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

AuthorMark Robinson <mark.robinson@imls.uzh.ch>, Dario Strbenac <dario.strbenac@sydney.edu.au>, Aaron Statham <a.statham@garvan.org.au>, Andrea Riebler <andrea.riebler@math.ntnu.no>
Date of publicationNone
MaintainerMark Robinson <mark.robinson@imls.uzh.ch>
LicenseLGPL (>= 2)
Version1.20.0

View on Bioconductor

Man pages

abcdDNA: A wrapper for fitting the offset-adjusted ABCD-DNA GLM

absoluteCN: Calculate and Segment Absolute Copy Number from Sequencing...

AdjustedCopyEstimate-class: Container for results of GC adjusted copy number estimation.

AffymetrixCdfFile-class: Placeholder For AffymetrixCdfFile Documentation

AffymetrixCelSet-class: Placeholder For AffymetrixCelSet Documentation

annoDF2GR: Convert a 'data.frame' to a 'GRanges'.

annoGR2DF: Convert an annotated 'GRanges' to a 'data.frame'.

annotationBlocksCounts: Counts the number of sequencing reads within supplied genomic...

annotationBlocksLookup: Forms a mapping between probe locations and chromosomal...

annotationCounts: Counts the number of sequencing reads surrounding supplied...

annotationLookup: Forms a mapping between probes on a tiling array and windows...

BAM2GRanges: Read in a (list of) BAM file(s) into a GRanges(List) object.

BayMethList-class: Class '"BayMethList"'

binPlots: Create line plots of averaged signal across a promoter

blocksStats: Calculate statistics for regions in the genome

checkProbes: Check Probe Specificity for Some Regions

chr21genes: Positions of Genes on Human Chromosome 21

ChromaBlocks: A function to find areas of enrichment in sequencing data

ChromaResults-class: ChromaResults class

chromosomeCNplots: Plot copy number by chromosome

ClusteredScoresList-class: Container for coverage matrices with clustering results.

clusterPlots: Visualisation of tables of feature coverages.

CopyEstimate-class: Container for results of fold change copy number estimation.

cpgBoxPlots: Boxplots of intensity, binned by Cpg Density

cpgDensityCalc: Calculate CpG Density in a Window

cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.

determineOffset: Function to determine the normalising offset f that accounts...

empBayes: Function to calculate prior parameters using empirical Bayes.

enrichmentCalc: Calculate sequencing enrichment

enrichmentPlot: Plot the distribution of sequencing enrichment.

expr: Vector of expression differences

FastQC-class: FastQC and associated classes

featureBlocks: Make windows for distances around a reference point.

featureScores: Get scores at regular sample points around genomic features.

findClusters: Find Clusters Epigenetically Modified Genes

GCadjustCopy: Calculate Absolute Copy Number from Sequencing Counts

GCAdjustParams-class: Container for parameters for mappability and GC content...

GCbiasPlots: Plot GC content vs. Read Counts Before Normalising, and GC...

gcContentCalc: Calculate The gcContent of a Region

genomeBlocks: Creates bins across a genome.

genQC: Plot Quality Checking Information for Sequencing Data

getProbePositionsDf: Translate Affymetrix probe information in a table.

getSampleOffsets: Calculates the sample-specific offsets, using the neutral...

hcRegions: Masking files for hg19

hyper: Gaussian hypergeometric function for vectorial arguments

loadPairFile: A routine to read Nimblegen tiling array intensities

loadSampleDirectory: A routine to read Nimblegen tiling array intensities

makeWindowLookupTable: Using the output of 'annotationLookup', create a tabular...

mappabilityCalc: Calculate The Mappability of a Region

MappabilitySource-class: Superclass for datatypes that can refer to genome mappability...

maskOut: Function to mask suspicious regions.

mergeReplicates: Merge GRanges that are of replicate experiments.

methylEst: Function to derive regional methylation estimates.

multiHeatmap: Superfigure plots

plotClusters: Plot Scores of Cluster Regions

plotQdnaByCN: Plotting the response of qDNA-seq data by CNV

processNDF: Reads in a Nimblegen microarray design file (NDF)

profilePlots: Create line plots of averaged signal across a promoter for...

QdnaData: A container for quantitative DNA sequencing data for ABCD-DNA...

regionStats: Find Regions of significance in microarray data

relativeCN: Calculate and Segment Relative Copy Number From Sequencing...

samplesList: Short Reads from Cancer and Normal

ScoresList-class: Container for 'featureScores()' output.

sequenceCalc: Find occurences of a DNA pattern

setCNVOffsets: Set the CNVOffsets of a 'QdnaData' object

summarizeScores: Subtract scores of different samples.

writeWig: Writes sequencing data out into wiggle files

Functions

abcdDNA Man page
absoluteCN Man page
absoluteCN,data.frame,matrix,GCAdjustParams-method Man page
absoluteCN,GRanges,matrix,GCAdjustParams-method Man page
AdjustedCopyEstimate Man page
AdjustedCopyEstimate-class Man page
AdjustedCopyEstimate,numeric,GRanges,numeric,numeric,matrix,list Man page
AffymetrixCdfFile Man page
AffymetrixCdfFile-class Man page
AffymetrixCelSet Man page
AffymetrixCelSet-class Man page
annoDF2GR Man page
annoDF2GR,data.frame-method Man page
annoGR2DF Man page
annoGR2DF,GRanges-method Man page
annotationBlocksCounts Man page
annotationBlocksCounts,ANY,data.frame-method Man page
annotationBlocksCounts,character,GRanges-method Man page
annotationBlocksCounts,GRanges,GRanges-method Man page
annotationBlocksCounts,GRangesList,GRanges-method Man page
annotationBlocksLookup Man page
annotationBlocksLookup,data.frame,data.frame-method Man page
annotationBlocksLookup,data.frame,GRanges-method Man page
annotationCounts Man page
annotationCounts,ANY,data.frame-method Man page
annotationCounts,ANY,GRanges-method Man page
annotationLookup Man page
annotationLookup,data.frame,data.frame-method Man page
annotationLookup,data.frame,GRanges-method Man page
BAM2GRanges Man page
BAM2GRanges,character-method Man page
BAM2GRangesList Man page
BAM2GRangesList,character-method Man page
Basic_Statistics Man page
Basic_Statistics,FastQC-method Man page
Basic_Statistics,SequenceQC-method Man page
Basic_Statistics,SequenceQCSet-method Man page
BayMethList Man page
[,BayMethList,ANY,missing,ANY-method Man page
BayMethList-class Man page
BayMethList,GRanges,matrix,matrix,numeric-method Man page
binPlots Man page
binPlots,ScoresList-method Man page
blocks Man page
blocks,ChromaResults-method Man page
blocksStats Man page
blocksStats,ANY,data.frame-method Man page
blocksStats,ANY,GRanges-method Man page
checkProbes Man page
checkProbes,data.frame,data.frame-method Man page
checkProbes,GRanges,GRanges-method Man page
chr21genes Man page
ChromaBlocks Man page
ChromaBlocks,GRangesList,GRangesList-method Man page
ChromaResults Man page
ChromaResults-class Man page
chromosomeCNplots Man page
chromosomeCNplots,AdjustedCopyEstimate-method Man page
chromosomeCNplots,CopyEstimate-method Man page
class:ChromaResults Man page
class:FastQC Man page
class:QdnaData Man page
class:RegionStats Man page
class:SequenceQC Man page
class:SequenceQCSet Man page
ClusteredScoresList Man page
[,ClusteredScoresList,ANY,missing,ANY-method Man page
ClusteredScoresList-class Man page
ClusteredScoresList,ScoresList-method Man page
clusterPlots Man page
clusterPlots,ClusteredScoresList-method Man page
clusterPlots,ScoresList-method Man page
clusters Man page
clusters,ClusteredScoresList-method Man page
control Man page
control<- Man page
control<-,BayMethList-method Man page
control,BayMethList-method Man page
CopyEstimate Man page
CopyEstimate-class Man page
CopyEstimate,GRanges,matrix,GRangesList,character-method Man page
cpgBoxplots Man page
cpgBoxplots,AffymetrixCelSet-method Man page
cpgBoxplots,matrix-method Man page
cpgDens Man page
cpgDens<- Man page
cpgDens<-,BayMethList-method Man page
cpgDens,BayMethList-method Man page
cpgDensityCalc Man page
cpgDensityCalc,data.frame,BSgenome-method Man page
cpgDensityCalc,GRanges,BSgenome-method Man page
cpgDensityCalc,GRangesList,BSgenome-method Man page
cpgDensityPlot Man page
cpgDensityPlot,GRangesList-method Man page
cutoff Man page
cutoff,ChromaResults-method Man page
determineOffset Man page
empBayes Man page
enrichmentCalc Man page
enrichmentCalc,GRangesList-method Man page
enrichmentCalc,GRanges-method Man page
enrichmentPlot Man page
enrichmentPlot,GRangesList-method Man page
expr Man page
FastQC-class Man page
FDRTable Man page
FDRTable,ChromaResults-method Man page
featureBlocks Man page
featureBlocks,data.frame-method Man page
featureBlocks,GRanges-method Man page
featureScores Man page
featureScores,ANY,data.frame-method Man page
featureScores,ANY,GRanges-method Man page
findClusters Man page
fOffset Man page
fOffset<- Man page
fOffset<-,BayMethList-method Man page
fOffset,BayMethList-method Man page
GCadjustCopy Man page
GCadjustCopy,data.frame,matrix,GCAdjustParams-method Man page
GCadjustCopy,GRanges,matrix,GCAdjustParams-method Man page
GCAdjustParams Man page
GCAdjustParams,BSgenome,MappabilitySource-method Man page
GCAdjustParams-class Man page
GCbiasPlots Man page
GCbiasPlots,AdjustedCopyEstimate-method Man page
gcContentCalc Man page
gcContentCalc,data.frame,BSgenome-method Man page
gcContentCalc,GRanges,BSgenome-method Man page
genomeBlocks Man page
genomeBlocks,BSgenome-method Man page
genomeBlocks,numeric-method Man page
genQC Man page
genQC,character-method Man page
genQC,SequenceQCSet-method Man page
getProbePositionsDf Man page
getProbePositionsDf,AffymetrixCdfFile-method Man page
getSampleOffsets Man page
hcRegions Man page
hyperg2F1_vec Man page
length Man page
length,BayMethList-method Man page
length,ScoresList-method Man page
loadPairFile Man page
loadSampleDirectory Man page
makeWindowLookupTable Man page
mappabilityCalc Man page
mappabilityCalc,data.frame,MappabilitySource-method Man page
mappabilityCalc,GRanges,MappabilitySource-method Man page
MappabilitySource Man page
MappabilitySource-class Man page
maskEmpBayes Man page
maskEmpBayes<- Man page
maskEmpBayes<-,BayMethList-method Man page
maskEmpBayes,BayMethList-method Man page
maskOut Man page
mergeReplicates Man page
mergeReplicates,GRangesList-method Man page
methEst Man page
methEst<- Man page
methEst<-,BayMethList-method Man page
methEst,BayMethList-method Man page
methylEst Man page
Mismatches Man page
Mismatches,SequenceQC-method Man page
Mismatches,SequenceQCSet-method Man page
MismatchTable Man page
MismatchTable,SequenceQC-method Man page
MismatchTable,SequenceQCSet-method Man page
multiHeatmap Man page
names<-,ScoresList-method Man page
names,ScoresList-method Man page
ncontrol Man page
ncontrol,BayMethList-method Man page
nsampleInterest Man page
nsampleInterest,BayMethList-method Man page
Overrepresented_sequences Man page
Overrepresented_sequences,FastQC-method Man page
Overrepresented_sequences,SequenceQC-method Man page
Overrepresented_sequences,SequenceQCSet-method Man page
Per_base_GC_content Man page
Per_base_GC_content,FastQC-method Man page
Per_base_GC_content,SequenceQC-method Man page
Per_base_GC_content,SequenceQCSet-method Man page
Per_base_N_content Man page
Per_base_N_content,FastQC-method Man page
Per_base_N_content,SequenceQC-method Man page
Per_base_N_content,SequenceQCSet-method Man page
Per_base_sequence_content Man page
Per_base_sequence_content,FastQC-method Man page
Per_base_sequence_content,SequenceQC-method Man page
Per_base_sequence_content,SequenceQCSet-method Man page
Per_base_sequence_quality Man page
Per_base_sequence_quality,FastQC-method Man page
Per_base_sequence_quality,SequenceQC-method Man page
Per_base_sequence_quality,SequenceQCSet-method Man page
Per_sequence_GC_content Man page
Per_sequence_GC_content,FastQC-method Man page
Per_sequence_GC_content,SequenceQC-method Man page
Per_sequence_GC_content,SequenceQCSet-method Man page
Per_sequence_quality_scores Man page
Per_sequence_quality_scores,FastQC-method Man page
Per_sequence_quality_scores,SequenceQC-method Man page
Per_sequence_quality_scores,SequenceQCSet-method Man page
plotClusters Man page
plotClusters,data.frame-method Man page
plotClusters,GRanges-method Man page
plotQdnaByCN Man page
priorTab Man page
priorTab<- Man page
priorTab<-,BayMethList-method Man page
priorTab,BayMethList-method Man page
processNDF Man page
profilePlots Man page
profilePlots,ScoresList-method Man page
QdnaData Man page
QdnaData-class Man page
readFastQC Man page
regions Man page
regions,ChromaResults-method Man page
regionStats Man page
regionStats,AffymetrixCelSet-method Man page
RegionStats-class Man page
regionStats,matrix-method Man page
relativeCN Man page
relativeCN,data.frame,matrix-method Man page
relativeCN,GRanges,matrix-method Man page
sampleInterest Man page
sampleInterest<- Man page
sampleInterest<-,BayMethList-method Man page
sampleInterest,BayMethList-method Man page
samplesList Man page
ScoresList Man page
[,ScoresList,ANY,missing,ANY-method Man page
ScoresList-class Man page
sequenceCalc Man page
sequenceCalc,data.frame,BSgenome-method Man page
sequenceCalc,GRanges,BSgenome-method Man page
Sequence_Duplication_Levels Man page
Sequence_Duplication_Levels,FastQC-method Man page
Sequence_Duplication_Levels,SequenceQC-method Man page
Sequence_Duplication_Levels,SequenceQCSet-method Man page
Sequence_Length_Distribution Man page
Sequence_Length_Distribution,FastQC-method Man page
Sequence_Length_Distribution,SequenceQC-method Man page
Sequence_Length_Distribution,SequenceQCSet-method Man page
SequenceQC-class Man page
SequenceQCSet Man page
[,SequenceQCSet,ANY,missing,ANY-method Man page
SequenceQCSet-class Man page
setCNVOffsets Man page
show,AdjustedCopyEstimate-method Man page
show,BayMethList-method Man page
show,ChromaResults-method Man page
show,ClusteredScoresList-method Man page
show,CopyEstimate-method Man page
show,FastQC-method Man page
show,QdnaData-method Man page
show,RegionStats-method Man page
show,ScoresList-method Man page
show,SequenceQC-method Man page
show,SequenceQCSet-method Man page
subsetRows Man page
subsetRows,ClusteredScoresList-method Man page
subsetRows,ScoresList-method Man page
summarizeScores Man page
summarizeScores,ScoresList,matrix-method Man page
tables Man page
tables,ScoresList-method Man page
windows Man page
windows<- Man page
windows<-,BayMethList-method Man page
windows,BayMethList-method Man page
writeWig Man page
writeWig,AffymetrixCelSet-method Man page
writeWig,GRangesList-method Man page

Files

Repitools/.Rinstignore
Repitools/DESCRIPTION
Repitools/NAMESPACE
Repitools/R
Repitools/R/BAM2GRanges.R Repitools/R/ChromaBlocks.R Repitools/R/FastQC-class.R Repitools/R/GCadjustCopy.R Repitools/R/GCbiasPlots.R Repitools/R/abcdDNA.R Repitools/R/absoluteCN.R Repitools/R/annoDF2GR.R Repitools/R/annoGR2DF.R Repitools/R/annotationLookup.R Repitools/R/binPlots.R Repitools/R/blocksStats.R Repitools/R/checkProbes.R Repitools/R/chromosomeCNplots.R Repitools/R/classes.R Repitools/R/clusterPlots.R Repitools/R/cpgBoxplots.R Repitools/R/cpgDensityCalc.R Repitools/R/cpgDensityPlot.R Repitools/R/determineOffset.R Repitools/R/empBayes.R Repitools/R/enrichmentCalc.R Repitools/R/enrichmentPlot.R Repitools/R/featureBlocks.R Repitools/R/featureScores.R Repitools/R/findClusters.R Repitools/R/gcContentCalc.R Repitools/R/genQC.R Repitools/R/genomeBlocks.R Repitools/R/getProbePositionsDf.R Repitools/R/hyper.R Repitools/R/makeWindowLookup.R Repitools/R/mappabilityCalc.R Repitools/R/maskOut.R Repitools/R/mergeReplicates.R Repitools/R/methylEst.R Repitools/R/multiHeatmap.R Repitools/R/plotClusters.R Repitools/R/processNimblegenArrays.R Repitools/R/profilePlots.R Repitools/R/regionStats.R Repitools/R/relativeCN.R Repitools/R/sequenceCalc.R Repitools/R/summarizeScores.R Repitools/R/utils.R Repitools/R/writeWig.R
Repitools/build
Repitools/build/vignette.rds
Repitools/data
Repitools/data/chr21genes.csv
Repitools/data/datalist
Repitools/data/expr.RData
Repitools/data/hcRegions.RData
Repitools/data/samplesList.RData
Repitools/inst
Repitools/inst/CITATION
Repitools/inst/doc
Repitools/inst/doc/Repitools_vignette.R
Repitools/inst/doc/Repitools_vignette.Rnw
Repitools/inst/doc/Repitools_vignette.pdf
Repitools/inst/examples
Repitools/inst/examples/annotationCounts_seq.R
Repitools/inst/examples/binPlots_affy.R
Repitools/inst/examples/binPlots_seq.R
Repitools/inst/examples/blockStats_affy.R
Repitools/inst/examples/clusterPlots_seq.R
Repitools/inst/examples/cpgDensityPlot_seq.R
Repitools/inst/examples/enrichmentPlot_seq.R
Repitools/inst/examples/featureScores_array.R
Repitools/inst/examples/featureScores_seq.R
Repitools/inst/examples/findClusters_dataframe.R
Repitools/inst/examples/mergeReplicates_seq.R
Repitools/inst/examples/regionStats_affy.R
Repitools/man
Repitools/man/AdjustedCopyEstimate-class.Rd Repitools/man/AffymetrixCdfFile-class.Rd Repitools/man/AffymetrixCelSet-class.Rd Repitools/man/BAM2GRanges.Rd Repitools/man/BayMethList-class.Rd Repitools/man/ChromaBlocks.Rd Repitools/man/ChromaResults-class.Rd Repitools/man/ClusteredScoresList-class.Rd Repitools/man/CopyEstimate-class.Rd Repitools/man/FastQC-class.Rd Repitools/man/GCAdjustParams-class.Rd Repitools/man/GCadjustCopy.Rd Repitools/man/GCbiasPlots.Rd Repitools/man/MappabilitySource-class.Rd Repitools/man/QdnaData.Rd Repitools/man/ScoresList-class.Rd Repitools/man/abcdDNA.Rd Repitools/man/absoluteCN.Rd Repitools/man/annoDF2GR.Rd Repitools/man/annoGR2DF.Rd Repitools/man/annotationBlocksCounts.Rd Repitools/man/annotationBlocksLookup.Rd Repitools/man/annotationCounts.Rd Repitools/man/annotationLookup.Rd Repitools/man/binPlots.Rd Repitools/man/blocksStats.Rd Repitools/man/checkProbes.Rd Repitools/man/chr21genes.Rd Repitools/man/chromosomeCNplots.Rd Repitools/man/clusterPlots.Rd Repitools/man/cpgBoxPlots.Rd Repitools/man/cpgDensityCalc.Rd Repitools/man/cpgDensityPlot.Rd Repitools/man/determineOffset.Rd Repitools/man/empBayes.Rd Repitools/man/enrichmentCalc.Rd Repitools/man/enrichmentPlot.Rd Repitools/man/expr.Rd Repitools/man/featureBlocks.Rd Repitools/man/featureScores.Rd Repitools/man/findClusters.Rd Repitools/man/gcContentCalc.Rd Repitools/man/genQC.Rd Repitools/man/genomeBlocks.Rd Repitools/man/getProbePositionsDf.Rd Repitools/man/getSampleOffsets.Rd Repitools/man/hcRegions.Rd Repitools/man/hyper.Rd Repitools/man/loadPairFile.Rd Repitools/man/loadSampleDirectory.Rd Repitools/man/makeWindowLookupTable.Rd Repitools/man/mappabilityCalc.Rd Repitools/man/maskOut.Rd Repitools/man/mergeReplicates.Rd Repitools/man/methylEst.Rd Repitools/man/multiHeatmap.Rd Repitools/man/plotClusters.Rd Repitools/man/plotQdnaByCN.Rd Repitools/man/processNDF.Rd Repitools/man/profilePlots.Rd Repitools/man/regionStats.Rd Repitools/man/relativeCN.Rd Repitools/man/samplesList.Rd Repitools/man/sequenceCalc.Rd Repitools/man/setCNVOffsets.Rd Repitools/man/summarizeScores.Rd Repitools/man/writeWig.Rd
Repitools/src
Repitools/src/Makevars
Repitools/src/Makevars.win
Repitools/src/Rexchange.h
Repitools/src/const.c
Repitools/src/hyp2f1.c
Repitools/src/mconf.h
Repitools/src/mtherr.c
Repitools/tests
Repitools/tests/tests.R
Repitools/vignettes
Repitools/vignettes/Repitools_vignette.Rnw
Repitools/vignettes/analyses1.tex
Repitools/vignettes/analyses2.tex
Repitools/vignettes/clusterPlot.png
Repitools/vignettes/datasets.tex
Repitools/vignettes/qc-cpgPlot.pdf
Repitools/vignettes/qc-enrPlot.pdf
Repitools/vignettes/qc.tex
Repitools/vignettes/readme.txt
Repitools/vignettes/rock1.png
Repitools/vignettes/sInfo.tex
Repitools/vignettes/utilities.tex
Repitools/vignettes/visualisations-binPlotsHeatmap.pdf
Repitools/vignettes/visualisations-binPlotsLine.pdf
Repitools/vignettes/visualisations-cluPlots3.pdf
Repitools/vignettes/visualisations-profPlots.pdf
Repitools/vignettes/visualisations.tex

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